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Protein Muffins Low Carb

4.89 from 26 votes
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This recipe may contain Amazon or other affiliate links. As an Amazon Associate I earn from qualifying purchases.

These Keto Low-Carb Protein Muffins are fluffy, moist chocolate muffins packed with 10 grams of proteins, no sugar or gluten, and guarantee to keep you full for hours.

Stack of Low-Carb Protein Muffins with white cases on a large plate.
Table of contents

I love to bake my low-carb breakfast, and since I work out every morning, I love adding proteins to my post-workout meal. I usually have my keto protein shake or a stack of my low-carb protein pancakes. But today, I was craving my keto chocolate muffin recipe, and I thought, how can I make high protein keto muffins?

So I decided to play in the kitchen and experiment with my favorite high-protein, low-carb ingredients: peanut butter, Nu Zest Chocolate Protein Powder, eggs, etc. The result is a fluffy, pure chocolate dream, and I can confidently claim that this is the beginning of a long list of low-carb protein muffin recipes! I am thinking about twisting my keto blueberry muffins into protein ones next time.

Why You Will Love These Protein Muffins (Low Carb)

  • Quick and easy to bake
  • Gluten-free
  • Sugar-free
  • Low-calories with only 145 kcal per serve
  • 10 grams protein each
  • Dairy-free option

Ingredients and Substitution

  • Chocolate Protein Powder – I am using chocolate pea isolate protein powder from NuZest. It’s a plant-based protein powder made in my country, and it’s wholesome and made with just 5 ingredients, no additives, or preservative. It’s sugar-free, low-carb, and taste amazing. You can also use whey protein powder, but you can’t use collagen protein powder for this recipe. Collagen powder won’t add texture in the muffins and it won’t firm up as well.
  • Unsweetened Cocoa Powder – To enhance the chocolate flavor of the muffins.
  • Erythritol – Feel free to use more if your protein powder is not very sweet in flavor, or decrease if you like the muffin less sweet. Watch out, if you decrease the sweetener, it might be bitter!
  • Almond Flour for texture, it makes the protein muffins moist and fluffy.
  • Baking Powder to rise the muffins.
  • Salt to balance the chocolate flavor.
  • Vanilla Extract for a sweet flavor.
  • Large Eggs – The size of eggs matters, if too small the batter end up super dry and thick.
  • Sugar-Free Chocolate Chips – Optional but it add a delicious sweet chocolate flavor, feel free to use milk chocolate or dark chocolate flavor depending on your taste.
  • Plain Greek Yogurt – I love using Greek yogurt in baking, like in my Greek yogurt brownies. This is a crucial ingredient to add proteins and moisture to these keto protein muffins. Plus, it’s low in carbs.
  • Natural Peanut Butter – with no added oil or added sugar. This boosts proteins, adds a lovely chocolate peanut butter flavor to the muffin, and it’s low-carb. Read more about how to make healthy homemade peanut butter if you need it.
  • Unsweetened Almond Milk or coconut milk if you prefer.

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Making Protein Muffins

Making Low-Carb Protein Muffins
  1. In a mixing bowl, whisk the wet ingredients: large eggs, yogurt, natural peanut butter, vanilla extract, unsweetened almond milk. It should be smooth with no lumps.
  2. Whisk in the remaining dry ingredients: chocolate protein powder, cocoa powder, sugar-free sweetener, and salt. The batter should be quick and thick but not dry.
Making Low-Carb Protein Muffins
  1. Fold in the chocolate chips and stir with a spatula to evenly incorporate.
  2. Preheat the oven to 350°F (180°C). Line a 12-hole muffin pan with 11 muffin paper liners and grease them with cooking oil spray. Fill each muffin liner with about 1/4 cup of protein muffin batter.
    Bake the muffins for 25 to 30 minutes until they are set on top, and a toothpick inserted in the center comes out clean.
    Remove them from the oven and cool down for 5 minutes in the muffin tin. Then, transfer to a cooling rack.

Expert Tips To Bake The Best Low-Carb Protein Muffins

  • Use pure protein powder – your blend should have a maximum of five ingredients: the source of the protein powder like pea protein isolate or whey protein then a sweetener, some natural flavor, and if chocolate powder, unsweetened cocoa is added too. You shouldn’t see a long list of ingredients in your protein powder or it means it’s not clean and it will certainly impact the protein muffin texture.
  • Don’t use collagen powder – collagen powder is not protein powder. They are two different ingredients. Protein powder firms up baked goods. It absorbs liquids and acts a bit like flour, such as in my keto protein bars. On the other hand, collagen powder has no impact on baking texture, except by adding a slight chew, but it will clearly not replace protein powder in these low-carb muffins.
  • Check baking time often – Protein powder muffins, like my keto protein cookies, bake super fast. Always watch them closely, inserting a pick in the center to check if they are set. If baked too long, they get dry.
  • Don’t swap almond flour for coconut flour. Keto baking with protein powder is tricky because low-carb protein powders absorb lots of liquid. If you add a little too much, you end up with dry muffins. So if you use coconut flour, which is the trickiest low-carb flour to bake with because it’s also so liquid absorbent, then you multiply the risks to end up with super dry protein muffins. So if you are a beginner at baking low-carb protein muffins, stick to almond flour; it adds moisture and it’s more forgiving.

More Low-Carb Muffin Recipes

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a chocolate protein muffins half bitten showing the fluffy texture and melted chocolate chips inside

Protein Muffins Low Carb

3.7gNet Carbs
These Keto Low-Carb Protein Muffins are fluffy, moist chocolate muffins packed with 10 grams of proteins, no sugar or gluten, and guarantee to keep you full for hours.
Prep: 10 minutes
Cook: 30 minutes
Total: 40 minutes
Yield: 11 muffins
Serving Size: 1 muffin (without chocolate chips)
4.89 from 26 votes


This recipe may contain Amazon or other affiliate links. As an Amazon Associate I earn from qualifying purchases.


  • Preheat the oven to 350°F (180°C). Line a 12-hole muffin tin with paper liners – I made only 11 muffins with this recipe. Spray cooking oil in each. Set aside.
  • In a large bowl, whisk the wet ingredients: eggs, yogurt, almond milk, peanut butter, and vanilla extract until smooth.
  • Whisk in dry ingredients: chocolate pea isolate protein powder, cocoa powder, salt, baking powder, and erythritol. The batter should be thick but not dry. If it looks dry and hard to stir, whisk in extra tablespoons of almond milk.
  • Fold in chocolate chips if used and stir to incorporate.
  • Fill the 11 muffin liners evenly and bake in the center rack of the oven for 20 to 25 minutes or until a toothpick inserted in the center comes out clean.
  • Cool down on a rack for an hour.


Storing the protein muffins 
  • Fridge – store in an airtight container for up to 4 days.
  • Freeze – place in zip-lock bags and freeze them for up to 1 month. Thaw at room temperature the day before.
Tried this recipe?Mention @sweetashoneyrecipes
Nutrition1 muffin (without chocolate chips)
Yield: 11 muffins


Serving: 1 muffin (without chocolate chips)Calories: 139.7 kcal (7%)Carbohydrates: 5.1 g (2%)Fiber: 1.4 g (6%)Net Carbs: 3.7 gProtein: 10 g (20%)Fat: 9.7 g (15%)Saturated Fat: 2 g (13%)Polyunsaturated Fat: 1.7 gMonounsaturated Fat: 3.6 gTrans Fat: 0.01 gCholesterol: 51.3 mg (17%)Sodium: 260.3 mg (11%)Potassium: 106.4 mg (3%)Sugar: 1.9 g (2%)Vitamin A: 79.6 IU (2%)Vitamin B12: 0.1 µg (2%)Vitamin D: 0.3 µg (2%)Calcium: 86.6 mg (9%)Iron: 1.8 mg (10%)Magnesium: 28.5 mg (7%)Zinc: 0.6 mg (4%)
Carine Claudepierre

About The Author

Carine Claudepierre

Hi, I'm Carine, the food blogger, author, recipe developer, published author of a cookbook and many ebooks, and founder of Sweet As Honey.

I have an Accredited Certificate in Nutrition and Wellness obtained in 2014 from Well College Global (formerly Cadence Health). I'm passionate about sharing all my easy and tasty recipes that are both delicious and healthy. My expertise in the field comes from my background in chemistry and years of following a keto low-carb diet. But I'm also well versed in vegetarian and vegan cooking since my husband is vegan.

I now eat a more balanced diet where I alternate between keto and a Mediterranean Diet

Cooking and Baking is my true passion. In fact, I only share a small portion of my recipes on Sweet As Honey. Most of them are eaten by my husband and my two kids before I have time to take any pictures!

All my recipes are at least triple tested to make sure they work and I take pride in keeping them as accurate as possible.

Browse all my recipes with my Recipe Index.

I hope that you too find the recipes you love on Sweet As Honey!

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    2 Thoughts On Protein Muffins Low Carb


The recipes, instructions, and articles on this website should not be taken or used as medical advice. You must consult with your doctor before starting on a keto or low-carb diet. The nutritional data provided on Sweetashoney is to be used as indicative only.

The nutrition data is calculated using WP Recipe Maker. Net Carbs is calculated by removing the fiber and some sweeteners from the total Carbohydrates. As an example, a recipe with 10 grams of Carbs per 100 grams that contains 3 grams of erythritol and 5 grams of fiber will have a net carbs content of 2 grams. Some sweeteners are excluded because they are not metabolized.

You should always calculate the nutritional data yourself instead of relying on Sweetashoney's data. Sweetashoney and its recipes and articles are not intended to cure, prevent, diagnose, or treat any disease. Sweetashoney cannot be liable for adverse reactions or any other outcome resulting from the use of recipes or advice found on the Website.